Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association

Authors

John Bannantine, USDA-ARSFollow
Chia-wei Wu, 2
Chungyi Hsu, 2
Shiguo Zhou, 3
David C. Schwartz, 3
Darrell O. Bayles, USDA-ARS National Animal Disease CenterFollow
Michael L. Paustian, USDA-ARSFollow
David P. Alt, 1
Srinand Sreevatsan, University of MinnesotaFollow
Vivek Kapur, USDA-ARSFollow
Adel M. Talaat, University of Wisconsin-Madison & Cairo UniversityFollow

Document Type

Article

Date of this Version

2012

Citation

Bannantine et al. BMC Genomics 2012, 13:89 http://www.biomedcentral.com/1471-2164/13/89

Comments

2012 Bannantine et al

Abstract

Background: The genome of Mycobacterium avium subspecies paratuberculosis (MAP) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map.

Results: Our analysis of one of the isolates, MAP S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the MAP S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human M. avium subsp. hominissuis strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb). Whole-genome sequencing of 2 additional sheep strains of MAP (JTC1074 and JTC7565) further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level.

Conclusions: Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the M. avium complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of MAP. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for M. avium complex strains based on these genome sequences.